AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID056_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391759
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	b0024	102	orf, hypothetical protein
#1	ileS	42	isoleucine tRNA synthetase
#2	pnp	177	polynucleotide phosphorylase; cytidylate kinase activity
#3	rpsO	148	30S ribosomal subunit protein S15
#4	rbfA	163	ribosome-binding factor A
#5	infB	24	protein chain initiation factor IF-2
#6	nusA	27	transcription pausing; L factor
#7	yhbC	300	orf, hypothetical protein

Motif 1
AATTAATTTTAAAAAGGGGCTAACAGCCCCT	4	121	1
TCTCCTGACAAAAAAGGGGCTGTTAGCCCCT	4	135	0
GTCAGCTTGAAAAAAGGGGCCACTCAGGCCC	2	32	0
CGAGTTTCAGAAAAGGGGGCCTGAGTGGCCC	2	16	1
AAACCCCGATAAATCGGGGCTTTATATAACT	7	223	0
CAAGACATAAAAAAAGGGCCTAAAGCCCAGT	7	276	0
TGACTACAGAATAACTGGGCTTTAGGCCCTT	7	263	1
TCGTCGGTTCAAATCCGGCCCCCGCAACCAC	7	80	1
ATCCATTGACAAAAGAAGGCTAAAAGGGCAT	0	60	0
          **** ******
MAP Score: 20.1678

Motif 2
CAATGGATTTGTGCAAATAAGCGCCGTTA      	0	83	1
TTGAAAAAAGGGGCCACTCAGGCCCCCTTTTCTGA	2	22	0
GTGGGTAAAGCCTCTCATTAGCCGCGCGAACCTCT	2	117	0
CTGGGTTAGGGTTGTCATTAGTCGCGAGG      	2	158	1
AACAATTTACGCGACGTTAAGCGGCAGTATTCTAC	3	43	0
TGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAAT	4	126	0
TAGTCTGGATGAGGTGAAAAGCCCGCG        	6	10	1
GTAGAATTTGCCACGTTTCAGGCGCGGGGTGGAGC	7	11	1
CGACGATCTTCGGGTTATGAGCCCGACGAGCTACC	7	51	0
AAGATCGTCGGTTCAAATCCGGCCCCCGCAACCAC	7	76	1
TTTTCAAATCCCACTACGAAGGCCGAAGTCTTCAC	7	141	0
TTATATAACTGAACCCTATAACCGCAACTGCGGTC	7	198	0
ATAGGGTTCAGTTATATAAAGCCCCGATTTATCGG	7	214	1
TACAGAATAACTGGGCTTTAGGCCCTTTTTTTATG	7	267	1
          * **   * ******
MAP Score: 10.0048

Motif 3
TATGGACAATTCAAAGGCCGAGGAATATGCC	0	34	1
AAATCCATTGACAAAAGAAGGCTAAAAGGGC	0	62	0
GGATTTGTGCAAATAAGCGCCGTTA      	0	87	1
TGCGAGTTTCAGAAAAGGGGGCCTGAGTGGC	2	14	1
CGTCAGCTTGAAAAAAGGGGCCACTCAGGCC	2	33	0
GTAAAGCCTCTCATTAGCCGCGCGAACCTCT	2	117	0
CGTCTTGCGATAACAGGTCGCTACGAGTAGA	3	17	1
GTATATAGAATGAAAGGACGCCGATCTCTAA	3	113	0
CACGTTGACCTGATAAGACGCGCCAGCGTCA	4	72	0
AAATTAATTTTAAAAAGGGGCTAACAGCCCC	4	120	1
TTCTCCTGACAAAAAAGGGGCTGTTAGCCCC	4	136	0
CTGGATGAGGTGAAAAGCCCGCG        	6	14	1
GGTTCAGTTATATAAAGCCCCGATTTATCGG	7	218	1
TAGTCAGATAACAAAAAACCCCGATAAATCG	7	238	0
CCAAGACATAAAAAAAGGGCCTAAAGCCCAG	7	277	0
          ******* ***
MAP Score: 8.55956

Motif 4
ATTCAAAGGCCGAGGAATATGCCCTTTTAGCCTTC	0	42	1
CAATGGATTTGTGCAAATAAGCGCCGTTA      	0	83	1
TGAAAAAAGGGGCCACTCAGGCCCCCTTTTCTGAA	2	21	0
CCCAGCTCTATGTGGGTAAAGCCTCTCATTAGCCG	2	128	0
GTCGCTACGAGTAGAATACTGCCGCTTAACGTCGC	3	33	1
GATCGCTGAATTAGAGATCGGCGTCCTTTCATTCT	3	103	1
AGGGTTCCATGCGGGATAAGGCGTTTACGCTGCAT	4	17	1
GGCAATCCATGCCGGATGCAGCGTAAACGCCTTAT	4	32	0
TTATCAGGTCAACGTGAACAGCCCTTCCACCTGAA	4	87	1
ATTTTAAAAAGGGGCTAACAGCCCCTTTTTTGTCA	4	126	1
TAGTCTGGATGAGGTGAAAAGCCCGCG        	6	10	1
TAGAATTTGCCACGTTTCAGGCGCGGGGTGGAGCA	7	12	1
AATATACTGTGAAGACTTCGGCCTTCGTAGTGGGA	7	133	1
ATAGGGTTCAGTTATATAAAGCCCCGATTTATCGG	7	214	1
ACAGAATAACTGGGCTTTAGGCCCTTTTTTTATGT	7	268	1
          *  *  * *******
MAP Score: 6.00001

Motif 5
GCTGCTCCACCCCGCGCCTGAAACGTGGCA	7	19	0
GTTTCAGAAAAGGGGGCCTGAGTGGCCCCT	2	19	1
AGGGCATATTCCTCGGCCTTTGAATTGTCC	0	37	0
ACTGTGAAGACTTCGGCCTTCGTAGTGGGA	7	138	1
AAAGTGGTTGCGGGGGCCGGATTTGAACCG	7	84	0
          CGCGGGCTTTTCACCTCATC	6	17	0
AATTAGAGATCGGCGTCCTTTCATTCTATA	3	111	1
ATAACCGCAACTGCGGTCTGGAGCACTTTC	7	186	0
GAGTAGAATACTGCCGCTTAACGTCGCGTA	3	41	1
TGCAGAGGTTCGCGCGGCTAATGAGAGGCT	2	114	1
CTACAGAATAACTGGGCTTTAGGCCCTTTT	7	266	1
GAATTGCTGCCGTCAGCTTGAAAAAAGGGG	2	44	0
        TAACGGCGCTTATTTGCACAAA	0	90	0
ACCCCGATAAATCGGGGCTTTATATAACTG	7	222	0
GTGAACAGCCCTTCCACCTGAAATTAATTT	4	100	1
AACCGACGATCTTCGGGTTATGAGCCCGAC	7	59	0
GCCCCGATTTATCGGGGTTTTTTGTTATCT	7	234	1
CCTGGTAGCTCGTCGGGCTCATAACCCGAA	7	48	1
          **********
MAP Score: 5.45536

Motif 6
GCTCTATGTGGGTAAAGCCTCTCATTAGCCGCGCGAACCTCTG	2	116	0
CATAGAGCTGGGTTAGGGTTGTCATTAGTCGCGAGG       	2	151	1
TCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACA     	3	5	0
GCTACGAGTAGAATACTGCCGCTTAACGTCGCGTAAATTGTTT	3	36	1
AACGTACACTGGGATCGCTGAATTAGAGATCGGCGTCCTTTCA	3	91	1
      AGTAGAATTTGCCACGTTTCAGGCGCGGGGTGGAGCA	7	4	1
GCGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCC	7	32	1
CTCATAACCCGAAGATCGTCGGTTCAAATCCGGCCCCCGCAAC	7	65	1
TCCTTCTGGAAAGTGCTCCAGACCGCAGTTGCGGTTATAGGGT	7	178	1
TGCGGTTATAGGGTTCAGTTATATAAAGCCCCGATTTATCGGG	7	207	1
ATCTGACTACAGAATAACTGGGCTTTAGGCCCTTTTTTTATGT	7	260	1
          *      ** *     ** ****
MAP Score: 3.76554

Motif 7
ATTCAAAGGCCGAGGAATATGCCCTTTTAGCCTT	0	42	1
CAGAAAAGGGGGCCTGAGTGGCCCCTTTTTTCAA	2	23	1
TTATCAGGTCAACGTGAACAGCCCTTCCACCTGA	4	87	1
ATTTTAAAAAGGGGCTAACAGCCCCTTTTTTGTC	4	126	1
TAGTCTGGATGAGGTGAAAAGCCCGCG       	6	10	1
CGACGATCTTCGGGTTATGAGCCCGACGAGCTAC	7	52	0
ATAGGGTTCAGTTATATAAAGCCCCGATTTATCG	7	214	1
ACATAAAAAAAGGGCCTAAAGCCCAGTTATTCTG	7	269	0
          ** ** *  *****
MAP Score: 3.18699

Motif 8
AAAAGAAGGCTAAAAGGGCATATTCCTCGGCCTTTGAATTGTCC	0	37	0
GAGTTTCAGAAAAGGGGGCCTGAGTGGCCCCTTTTTTCAAGCTG	2	17	1
CTCCTGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAATT	4	121	0
GCCTGGTAGCTCGTCGGGCTCATAACCCGAAGATCGTCGGTTCA	7	47	1
TCGTCGGTTCAAATCCGGCCCCCGCAACCACTTTCCCTTAGAGT	7	80	1
CAAGACATAAAAAAAGGGCCTAAAGCCCAGTTATTCTGTAGTCA	7	263	0
          ***  ****        *    **
MAP Score: 1.23898

Motif 9
CAGAAAAGGGGGCCTGAGTGGCCCCTTTTTTCAAGCTG	2	23	1
GACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAAT	4	122	0
GTTCAAATCCGGCCCCCGCAACCACTTTCCCTTAGAGT	7	86	1
CAGAATAACTGGGCTTTAGGCCCTTTTTTTATGTCTTG	7	269	1
          ****     * **  ***
MAP Score: 1.19627

Motif 10
GTTTCAGAAAAGGGGGCCTGAGTGGCCCCTTTTTTCAAGCT	2	19	1
TTTACGCTGCATCCGGCATGGATTGCCTGATGTGACGCTGG	4	40	1
ATTAATTTTAAAAAGGGGCTAACAGCCCCTTTTTTGTCAGG	4	122	1
ACGTTTCAGGCGCGGGGTGGAGCAGCCTGGTAGCTCGTCGG	7	23	1
AACCGACGATCTTCGGGTTATGAGCCCGACGAGCTACCAGG	7	48	0
CTCTAAGGGAAAGTGGTTGCGGGGGCCGGATTTGAACCGAC	7	82	0
ACTACAGAATAACTGGGCTTTAGGCCCTTTTTTTATGTCTT	7	265	1
          *   *** *  *  ***   *
MAP Score: 0.333602